The "charge" is not just magnetic coils magnetizing.
How circular accelerators typically work is - the particle gets injected (sometimes coming out of a pre-accelerator) and then gains energy over multiple (many) loops.
If there is indeed a projectile already in the loop, just depowering the magnets would be rather awkward, so the safest option might indeed be to discharge it the "normal" way
Someone mentioned the clearing bucket on a firing range in some of the recent (unrelated) discussions - sometimes discharging a weapon is the safest option. So presumably before going into menu (or for a drink) the pilot should safely discharge the Gungnir.
Although i can also see the argument for player comfort and QoL should take precedence over realism.
We could just invent some safe discharge mode, where the projectile gets expelled at lower power, but then the coils have to go though a full discharge and cooldown cycle, causing some extra delay before being ready to go again (i think it's what ButItRuns might be getting at).